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Use Artifacts.toml to access VARNA jar file #12

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merged 3 commits into from
Jun 27, 2023
Merged

Use Artifacts.toml to access VARNA jar file #12

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187fe55
Use Artifacts.toml to access VARNA jar file
marcom Jun 27, 2023
5837f5f
Have to use LazyArtifacts for a lazy artifact
marcom Jun 27, 2023
f22ff3e
Improve README for java and artifacts instructions
marcom Jun 27, 2023
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7 changes: 7 additions & 0 deletions Artifacts.toml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
[VARNAv3-93_jar]
git-tree-sha1 = "7141dcd09e8fced75b19ca928bd4a790af61ffc2"
lazy = true

[[VARNAv3-93_jar.download]]
sha256 = "58e19c60214ca15f8aefe91ba0feafde3c21b2f30700d8b5b718a3c5bf7aaa5d"
url = "https://gist.github.com/marcom/e9f305a65fc6fbd0fef6df2d66d92f88/raw/7141dcd09e8fced75b19ca928bd4a790af61ffc2.tar.gz"
3 changes: 1 addition & 2 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,11 @@ version = "0.3.0"
[deps]
BioStockholm = "eeb925a3-6f9d-43e6-829e-e0ea03b76ecf"
ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
Luxor = "ae8d54c2-7ccd-5906-9d76-62fc9837b5bc"
PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
R2R_jll = "1e27f72a-4876-5c10-8678-3341fdb8ba55"
Requires = "ae029012-a4dd-5104-9daa-d747884805df"
Scratch = "6c6a2e73-6563-6170-7368-637461726353"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
ViennaRNA = "05a721ad-238d-4945-8c85-8b5c1fff3465"

Expand All @@ -31,7 +31,6 @@ Luxor = "3.3"
PrecompileTools = "1"
R2R_jll = "=1.0.6"
Requires = "1.3"
Scratch = "1.1"
UnicodePlots = "3"
ViennaRNA = "0.11"
julia = "1.6"
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10 changes: 5 additions & 5 deletions README.md
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Expand Up @@ -109,14 +109,14 @@ VARNA.plot_compare(dbn1="(((.....)))", seq1="GCGAAAAACGC",
You will need a working Java installation (can be headless i think).
You can test this by running:
```julia
run(`java -version`)
Sys.which("java")
```
If you don't get an error, plotting with VARNA should work.
If you get a file path (e.g. `"/usr/bin/java"`) and not `nothing`,
plotting with VARNA should work.

The VARNA jar file will get downloaded automatically the first time
you plot something with VARNA. It gets stored in a scratch space that
gets cleaned up by the Julia package manager when you uninstall
PlotRNA.
you plot something with one of the VARNA functions. It gets stored in
the Julia artifacts directory.


#### VARNA plot options
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26 changes: 5 additions & 21 deletions src/varna.jl
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Expand Up @@ -5,25 +5,9 @@ module VARNA
# `-foo` : error, no argument for option foo
# `-foo bar` : no error or warning

using Scratch: @get_scratch!

const _download_url = "https://varna.lri.fr/bin/VARNAv3-93.jar"

# this will be filled in by `__init__()`
_download_cache = ""

function __init__()
global _download_cache = @get_scratch!("jar")
end

function _download_varna_jar(url=_download_url)
fname = joinpath(_download_cache, basename(url))
if !isfile(fname)
@info "downloading VARNA jar file from $url"
download(url, fname)
end
return fname
end
# TODO, this doesn't work: using LazyArtifacts: @artifact_str
using LazyArtifacts
_get_varna_jar() = artifact"VARNAv3-93_jar/VARNAv3-93.jar"

# VARNA-3.93 supported formats: JPEG,PNG,EPS,XFIG,SVG
const _map_fileendings_to_mime = Dict(
Expand Down Expand Up @@ -187,7 +171,7 @@ function plot(dbn::AbstractString;
fileformat::AbstractString="svg",
verbose::Bool=false,
plot_opts...)
varna_jarpath = _download_varna_jar()
varna_jarpath = _get_varna_jar()
if length(dbn) != length(seq)
throw(ArgumentError("structure and sequence must have same length: $(length(dbn)) != $(length(seq))"))
end
Expand Down Expand Up @@ -226,7 +210,7 @@ function plot_compare(; dbn1::AbstractString,
fileformat::AbstractString="svg",
verbose::Bool=false,
plot_opts...)
varna_jarpath = _download_varna_jar()
varna_jarpath = _get_varna_jar()
if length(dbn1) != length(dbn2) || length(dbn1) != length(seq1) || length(dbn1) != length(seq2)
throw(ArgumentError("all structures and sequences must have same length, here they are: " *
"dbn1=$(length(dbn1)), seq1=$(length(seq1)), dbn2=$(length(dbn2)), seq2=$(length(seq2)))"))
Expand Down